I recently "upgraded" to XCode 5.2 and now a number of R packages will not work. I have a 15" MBP running OSX Mavericks 10.9.1 and am running R 3.0.2.

First, the mcmc function in the package diversitree broke and gave the following error:

    Error in .External(list(name = "CppMethod__invoke_notvoid", address = <pointer: 0x0>,  : 
      NULL value passed as symbol address

Furthermore, I cannot compile the package "geomorph" from source, and I get the following error:

    clang: error: no such file or directory: 'SHLIB_LIBADD'
    clang: error: no such file or directory: '='
    make: *** [geomorph.so] Error 1
    ERROR: compilation failed for package ‘geomorph’

So I believe the error is somewhere in the compilers. I tested this idea with:

    > require(Rcpp)
    > evalCpp("1+1")
    clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include  -I"/Users/Chris/Library/R/3.0/library/Rcpp/include"    -fPIC  "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c file177c642d0b53.cpp -o file177c642d0b53.o clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o sourceCpp_1783.so file177c642d0b53.o /Users/Chris/Library/R/3.0/library/Rcpp/lib/libRcpp.a SHLIB_LIBADD = -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation 
    Error in sourceCpp(code = code, env = env, rebuild = rebuild, showOutput = showOutput,  : 
      Error 1 occurred building shared library.
    
    WARNING: The tools required to build C++ code for R were not found.
    
    Please install Command Line Tools for XCode (or equivalent).
    
    clang: error: no such file or directory: 'SHLIB_LIBADD'
    clang: error: no such file or directory: '='
    make: *** [sourceCpp_1783.so] Error 1

Also this:

    has_devel()
    '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla  \
      CMD SHLIB foo.c 

    clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  "-mtune=native -g -O2 -Wall -pedantic -Wconversion" -c foo.c -o foo.o
    clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o foo.so foo.o SHLIB_LIBADD = -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
    clang: error: no such file or directory: 'SHLIB_LIBADD'
    Error: Command failed (1)
    clang: error: no such file or directory: '='
    make: *** [foo.so] Error 1

I tried reinstalling Rcpp from source and that fails too:

    clang: error: no such file or directory: 'SHLIB_LIBADD'
    clang: error: no such file or directory: '='
    make: *** [Rcpp.so] Error 1

I've spent hours now trying to troubleshoot this and I've run across numerous mentions of editing the Makeconf file to add clang. I have done this but still cannot get things that use C in R to work.

I believe the error is in the SHLIB_LIBADD line of the Makeconf file. If I change it to something like: 

-L/usr/lib/R/lib

I can compile packages, but some of the functions do no work.  I would greatly appreciate any help.

Chris


-- 
Christopher Hamm
Postdoctoral Scholar
Department of Evolution and Ecology
University of California, Davis
3347 Storer Hall
One Shields Ave.
Davis, California 95616
USA

email: cahamm@ucdavis.edu
lab phone: (530) 754-9551 
http://www.eve.ucdavis.edu/cahamm
http://pizzabeerandscience.blogspot.com/


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